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- PDB-2lam: Three-dimensional structure of the cyclotide Cter M -

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Basic information

Entry
Database: PDB / ID: 2lam
TitleThree-dimensional structure of the cyclotide Cter M
ComponentsCyclotide Cter M
KeywordsANTIVIRAL PROTEIN / Insecticidal peptide
Function / homology
Function and homology information


defense response / killing of cells of another organism / extracellular region
Similarity search - Function
Albumin I chain a / Albumin I chain a / Cyclotide, moebius, conserved site / Cyclotides Moebius subfamily signature. / Cyclotides profile. / Cyclotide / Cyclotide superfamily / Cyclotide family
Similarity search - Domain/homology
Biological speciesClitoria ternatea (plant)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model 1
AuthorsPoth, A.G. / Colgrave, M.L. / Lyons, R.E. / Daly, N.L. / Craik, D.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: From the Cover: Discovery of an unusual biosynthetic origin for circular proteins in legumes.
Authors: Poth, A.G. / Colgrave, M.L. / Lyons, R.E. / Daly, N.L. / Craik, D.J.
History
DepositionMar 16, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 18, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cyclotide Cter M


Theoretical massNumber of molelcules
Total (without water)3,0851
Polymers3,0851
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Cyclotide Cter M


Mass: 3084.610 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Clitoria ternatea (plant) / References: UniProt: P86899*PLUS
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
1212D 1H-1H NOESY
1312D DQF-COSY

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Sample preparation

DetailsContents: 1 mM Cter M, 70% H2O/20%CD3CN/10% D2O / Solvent system: 70% H2O/20%CD3CN/10% D2O
SampleConc.: 1 mM / Component: Cter M-1
Sample conditionsIonic strength: ambient / pH: 4 / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE9001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
XEASYBartels et al.chemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CNSSOLVEBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSSOLVEBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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